Changeset 71
- Timestamp:
- Jun 17, 2011, 2:58:20 PM (8 years ago)
- Location:
- trunk
- Files:
-
- 12 edited
-
grails-app/controllers/nl/tno/massSequencing/AssayController.groovy (modified) (1 diff)
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grails-app/controllers/nl/tno/massSequencing/AssaySampleController.groovy (modified) (2 diffs)
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grails-app/controllers/nl/tno/massSequencing/FastaController.groovy (modified) (2 diffs)
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grails-app/controllers/nl/tno/massSequencing/RunController.groovy (modified) (3 diffs)
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grails-app/views/assay/index.gsp (modified) (1 diff)
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grails-app/views/assay/show.gsp (modified) (1 diff)
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grails-app/views/assaySample/show.gsp (modified) (2 diffs)
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grails-app/views/query/index.gsp (modified) (2 diffs)
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grails-app/views/run/index.gsp (modified) (1 diff)
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grails-app/views/run/show.gsp (modified) (1 diff)
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web-app/css/query.css (modified) (1 diff)
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web-app/js/query.js (modified) (5 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/grails-app/controllers/nl/tno/massSequencing/AssayController.groovy
r70 r71 127 127 128 128 // Send the assay information to the view 129 [assay: assay, editable: assay.study.canWrite( session.user ), otherRuns: otherRuns, "numClassified": numClassified ? numClassified[ 0 ]: 0]129 [assay: assay, editable: assay.study.canWrite( session.user ), otherRuns: otherRuns, "numClassified": numClassified ? ( numClassified[ 0 ] ?: 0 ) : 0] 130 130 } 131 131 -
trunk/grails-app/controllers/nl/tno/massSequencing/AssaySampleController.groovy
r70 r71 3 3 import java.util.List; 4 4 import org.codehaus.groovy.grails.commons.ConfigurationHolder 5 import nl.tno.massSequencing.classification.Classification 5 6 6 7 class AssaySampleController { … … 27 28 } 28 29 29 30 [assaySample: assaySample, entityType: params.entityType] 30 // Determine the number of classifications for this sample 31 def numClassifications = Classification.executeQuery( "SELECT SUM( c.unclassified ) FROM Classification c WHERE c.assaySample = :assaySample", [ "assaySample": assaySample ] ) 32 33 [assaySample: assaySample, entityType: params.entityType, numClassifications: numClassifications ? ( numClassifications[ 0 ] ?: 0 ) : 0 ] 31 34 } 32 35 -
trunk/grails-app/controllers/nl/tno/massSequencing/FastaController.groovy
r63 r71 9 9 def fastaService 10 10 def sessionFactory 11 def classificationService 11 12 12 13 def deleteData = { … … 53 54 // Recalculate the number of sequences for this sample 54 55 AssaySample.recalculateNumSequences( sample ); 56 57 // Update classification since some sequences have been removed 58 classificationService.updateClassificationForAssaySample( sample ); 55 59 56 60 flash.message = numFiles + " file" + (numFiles != 1 ? "s have" : " has" ) + " been deleted from this sample" -
trunk/grails-app/controllers/nl/tno/massSequencing/RunController.groovy
r70 r71 14 14 def fastaService 15 15 def dataTablesService 16 def classificationService 16 17 17 18 def index = { … … 114 115 115 116 // Send the assay information to the view 116 [run: run, allRuns: Run.list(), otherAssays: otherAssays, editable: true, "numClassified": numClassified ? numClassified[ 0 ]: 0 ]117 [run: run, allRuns: Run.list(), otherAssays: otherAssays, editable: true, "numClassified": numClassified ? ( numClassified[ 0 ] ?: 0 ) : 0 ] 117 118 } 118 119 … … 797 798 def numFiles = fastaService.deleteSequenceData( assaySamples ); 798 799 800 // Reset classification for given samples 801 classificationService.updateClassificationForAssaySample( assaySamples ); 802 799 803 flash.message = numFiles + " files have been removed from the run."; 800 804 redirect( controller: 'run', action: 'show', id: run.id ); -
trunk/grails-app/views/assay/index.gsp
r70 r71 36 36 </table> 37 37 <p class="options"> 38 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink action="exportAsFasta" />', '#assays', 'Please select an assay to export' ); return false;">Export a s fasta</a>38 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink action="exportAsFasta" />', '#assays', 'Please select an assay to export' ); return false;">Export all data</a> 39 39 <a class="excel" href="#" onClick="submitPaginatedForm( $( '#assayForm' ), '<g:createLink action="exportMetaData" />', '#assays', 'Please select an assay to export' ); return false;">Export metadata</a> 40 40 </p> -
trunk/grails-app/views/assay/show.gsp
r70 r71 118 118 119 119 <p class="options multiple"> 120 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportAsFasta" />', '#samples', 'Please select one or more samples to export' ); return false;">Export a s fasta</a><br />120 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportAsFasta" />', '#samples', 'Please select one or more samples to export' ); return false;">Export all data</a><br /> 121 121 <a class="excel" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportMetaData" />', '#samples', 'Please select one or more samples to export' ); return false;">Export metadata</a><br /> 122 122 <a class="classification_export" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="classification" action="export" />', '#samples', 'Please select one or more samples to export' ); return false;">Export classification</a><br /> -
trunk/grails-app/views/assaySample/show.gsp
r56 r71 12 12 <ul class="blok_data"> 13 13 <li><label># sequences</label><span class="value">${assaySample.numSequences() ?: '-'}</span></li> 14 <li><label># unique sequences</label><span class="value">${assaySample.numUniqueSequences ?: '-'}</span></li> 15 </ul> 14 <li><label># qual scores</label><span class="value">${assaySample.numQualScores() ?: '-'}</span></li> 15 <li><label>% classified</label><span class="value"> 16 <g:if test="${assaySample.numSequences > 0}"> 17 <g:formatNumber number="${numClassifications / assaySample.numSequences}" format="0.0%" /> 18 </g:if> 19 <g:else> 20 - 21 </g:else> 22 </span></li> 23 </ul> 16 24 17 <h2> Details</h2>25 <h2>Amplicon details</h2> 18 26 <ul class="assaySampleDetails"> 19 27 <li class="title"> … … 50 58 51 59 <g:if test="${assaySample.sequenceData?.size()}"> 52 <h2> Files</h2>60 <h2>Sequences</h2> 53 61 <table class="paginate"> 54 62 <thead> -
trunk/grails-app/views/query/index.gsp
r66 r71 74 74 Operator 75 75 </span> 76 <span class="operator"> 76 <span class="value"> 77 Value 78 </span> 79 <span class="combinator">or</span> 80 <span class="factor"> 77 81 Factor 82 </span> 83 <span class="othertaxon"> 84 Other taxon 78 85 </span> 79 <span class="combinedValue">80 <span class="item">Value</span>81 <span class="combinator">or</span>82 <span class="item">Other taxon</span>83 </span>84 86 </li> 85 87 <li class="newCriterion"> … … 103 105 </select> 104 106 </span> 107 <span class="value"> 108 <input class='text' type="text" id="value" onChange="toggleValueAndTaxonInput();" name="criteria.0.value" /> 109 </span> 110 <span class="combinator">or</span> 105 111 <span class="factor"> 106 <input class='text' type="text" id="factor" name="criteria.0.factor" />112 <input class='text' type="text" id="factor" onChange="toggleValueAndTaxonInput();" name="criteria.0.factor" /> 107 113 </span> 108 <span class="combinedValue"> 109 <input class='text' type="text" id="value" onChange="toggleValueAndTaxonInput();" name="criteria.0.value" /> 110 <span class="combinator">or</span> 114 <span class="othertaxon"> 111 115 <input class='text' type="text" id="otherTaxonText" onChange="toggleValueAndTaxonInput();" name="criteriataxon" /> 112 116 <input type="hidden" name="criteria.0.othertaxon" id="otherTaxonValue"/> -
trunk/grails-app/views/run/index.gsp
r70 r71 47 47 <p class="options"> 48 48 <a class="add" href="#" onClick="showAddRunDialog(); return false;">Add run</a> 49 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#runForm' ), '<g:createLink action="exportAsFasta" />', '#runs', 'Please select a run to export' ); return false;">Export a s fasta</a>49 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#runForm' ), '<g:createLink action="exportAsFasta" />', '#runs', 'Please select a run to export' ); return false;">Export all data</a> 50 50 <a class="excel" href="#" onClick="submitPaginatedForm( $( '#runForm' ), '<g:createLink action="exportMetaData" />', '#runs', 'Please select a run to export' ); return false;">Export metadata</a> 51 51 </p> -
trunk/grails-app/views/run/show.gsp
r70 r71 164 164 <p class="options multiple"> 165 165 <g:if test="${numReadableAssaySamples > 0}"> 166 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportAsFasta" />', '#samples', 'Please select one or more samples to export' ); return false;">Export a s fasta</a><br />166 <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportAsFasta" />', '#samples', 'Please select one or more samples to export' ); return false;">Export all data</a><br /> 167 167 <a class="excel" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportMetaData" />', '#samples', 'Please select one or more samples to export' ); return false;">Export metadata</a><br /> 168 168 <a class="classification_export" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="classification" action="export" />', '#samples', 'Please select one or more samples to export' ); return false;">Export classification</a><br /> -
trunk/web-app/css/query.css
r66 r71 21 21 #searchForm ul#criteria li .factor input { width: 60px; } 22 22 23 #searchForm ul#criteria li .combinedValue { width: 340px; font-weight: normal; } 24 #searchForm ul#criteria li .combinedValue span.item { vertical-align: bottom; width: 140px; font-weight: bold; } 25 #searchForm ul#criteria li .combinedValue input { width: 140px; } 23 #searchForm ul#criteria li span.combinator { width: 16px; font-weight: normal; } 26 24 27 #searchForm ul#criteria li span.combinator { vertical-align: bottom; width: 16px; } 25 #searchForm ul#criteria li .value { width: 160px; } 26 #searchForm ul#criteria li .value input { width: 140px; } 28 27 29 #searchForm ul#criteria li .value { width: 140px; } 30 #searchForm ul#criteria li .othertaxon { width: 165px; } 31 28 #searchForm ul#criteria li .othertaxon { width: 160px; } 29 #searchForm ul#criteria li .othertaxon input { width: 140px; } 32 30 33 31 #searchForm ul#criteria li .addButton { margin: 4px 0; } -
trunk/web-app/js/query.js
r66 r71 118 118 $( '#otherTaxonValue' ).val( '' ); 119 119 $( '#otherTaxonText' ).attr( 'disabled', true ); 120 } else if( $( '#otherTaxonText' ).val() != "" ) { 120 121 $( '#factor' ).val( '' ); 122 $( '#factor' ).attr( 'disabled', true ); 123 } else if( $( '#otherTaxonText' ).val() != "" || $( '#factor' ).val() != "" ) { 121 124 // Disable value input 122 125 $( '#value' ).val( '' ); … … 126 129 $( '#value' ).attr( 'disabled', false ); 127 130 $( '#otherTaxonText' ).attr( 'disabled', false ); 131 $( '#factor' ).attr( 'disabled', false ); 128 132 } 129 133 } … … 197 201 var fieldSpan = createCriterionElement( 'entity', entity ); 198 202 var operatorSpan = createCriterionElement( 'operator', operator ); 199 var factorSpan = createCriterionElement( 'factor', "" );200 203 var valueSpan = createInSearchElement( 'value', value ); 204 var whitespaceSpan = createCriterionElement( 'whitespace', "" ); 201 205 202 206 var input = $( '<a href="#" onClick="return false;"><img src="' + baseUrl + '/plugins/famfamfam-1.0.1/images/icons/delete.png" border="0"></a>' ); … … 215 219 // Append them to a list item 216 220 var li = $( '<li></li>' ); 217 li.append( fieldSpan ).append( "\n" ).append( operatorSpan ).append( "\n" ).append( factorSpan ).append( "\n" ).append( valueSpan ).append( "\n" ).append( span ); 221 li.append( fieldSpan ).append( "\n" ) 222 .append( operatorSpan ).append( "\n" ) 223 .append( valueSpan ).append( "\n" ) 224 .append( $( '<span class="combinator"></span>') ).append( "\n" ) 225 .append( $( '<span class="factor"></span>') ).append( "\n" ) 226 .append( $( '<span class="othertaxon"></span>') ).append( "\n" ) 227 .append( span ); 218 228 219 229 $('#criteria .newCriterion').before(li); … … 248 258 // Append them to a list item 249 259 var li = $( '<li></li>' ); 250 li.append( fieldSpan ).append( "\n" ).append( operatorSpan ).append( "\n" ).append( factorSpan ).append( "\n" ).append( valueSpan ).append( "\n" ).append( orSpan ).append( "\n" ).append( otherTaxonSpan ).append( "\n" ).append( span ); 260 li.append( fieldSpan ).append( "\n" ) 261 .append( operatorSpan ).append( "\n" ) 262 .append( valueSpan ).append( "\n" ) 263 .append( orSpan ).append( "\n" ) 264 .append( factorSpan ).append( "\n" ) 265 .append( otherTaxonSpan ).append( "\n" ) 266 .append( span ); 251 267 252 268 $('#criteria .newCriterion').before(li);
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